But when i run the program i get the following issues:
Using Theano backend.
Traceback (most recent call last):
File "/cvmfs/soft.HPC/easybuild/software/2017/Core/python/3.6.3/lib/python3.6/configparser.py", line 1138, in _unify_values
sectiondict = self._sections[section]
KeyError: 'blas'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/home/USER/deepvirfinder_env/lib/python3.6/site-packages/theano/configparser.py", line 168, in fetch_val_for_key
return theano_cfg.get(section, option)
File "/cvmfs/soft.HPC/easybuild/software/2017/Core/python/3.6.3/lib/python3.6/configparser.py", line 781, in get
d = self._unify_values(section, vars)
File "/cvmfs/soft.HPC/easybuild/software/2017/Core/python/3.6.3/lib/python3.6/configparser.py", line 1141, in _unify_values
raise NoSectionError(section)
configparser.NoSectionError: No section: 'blas'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/home/USER/deepvirfinder_env/lib/python3.6/site-packages/theano/configparser.py", line 328, in get
delete_key=delete_key)
File "/home/USER/deepvirfinder_env/lib/python3.6/site-packages/theano/configparser.py", line 172, in fetch_val_for_key
raise KeyError(key)
KeyError: 'blas.ldflags'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/home/USER/deepvirfinder_env/lib/python3.6/site-packages/theano/configdefaults.py", line 1250, in check_mkl_openmp
import mkl
ModuleNotFoundError: No module named 'mkl'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/home/USER/deepvirfinder_env/bin/DeepVirFinder/dvf.py", line 53, in
import keras
File "/home/USER/deepvirfinder_env/lib/python3.6/site-packages/keras/init.py", line 3, in
from . import utils
File "/home/USER/deepvirfinder_env/lib/python3.6/site-packages/keras/utils/init.py", line 6, in
from . import conv_utils
File "/home/USER/deepvirfinder_env/lib/python3.6/site-packages/keras/utils/conv_utils.py", line 9, in
from .. import backend as K
File "/home/USER/deepvirfinder_env/lib/python3.6/site-packages/keras/backend/init.py", line 1, in
from .load_backend import epsilon
File "/home/USER/deepvirfinder_env/lib/python3.6/site-packages/keras/backend/load_backend.py", line 87, in
from .theano_backend import *
File "/home/USER/deepvirfinder_env/lib/python3.6/site-packages/keras/backend/theano_backend.py", line 7, in
import theano
File "/home/USER/deepvirfinder_env/lib/python3.6/site-packages/theano/init.py", line 124, in
from theano.scan_module import (scan, map, reduce, foldl, foldr, clone,
File "/home/USER/deepvirfinder_env/lib/python3.6/site-packages/theano/scan_module/init.py", line 41, in
from theano.scan_module import scan_opt
File "/home/USER/deepvirfinder_env/lib/python3.6/site-packages/theano/scan_module/scan_opt.py", line 60, in
from theano import tensor, scalar
File "/home/USER/deepvirfinder_env/lib/python3.6/site-packages/theano/tensor/init.py", line 17, in
from theano.tensor import blas
File "/home/USER/deepvirfinder_env/lib/python3.6/site-packages/theano/tensor/blas.py", line 155, in
from theano.tensor.blas_headers import blas_header_text
File "/home/USER/deepvirfinder_env/lib/python3.6/site-packages/theano/tensor/blas_headers.py", line 987, in
if not config.blas.ldflags:
File "/home/USER/deepvirfinder_env/lib/python3.6/site-packages/theano/configparser.py", line 332, in get
val_str = self.default()
File "/home/USER/deepvirfinder_env/lib/python3.6/site-packages/theano/configdefaults.py", line 1430, in default_blas_ldflags
check_mkl_openmp()
File "/home/USER/deepvirfinder_env/lib/python3.6/site-packages/theano/configdefaults.py", line 1262, in check_mkl_openmp
""")
RuntimeError:
Could not import 'mkl'. Either install mkl-service with conda or set
MKL_THREADING_LAYER=GNU in your environment for MKL 2018.
If you have MKL 2017 install and are not in a conda environment you
can set the Theano flag blas.check_openmp to False. Be warned that if
you set this flag and don't set the appropriate environment or make
sure you have the right version you will get wrong results.
Hi there,
Is there a way to have DeepVirFinder available through singularity or docker? I am working on an HPC and conda is not allowed as it causes conflicts.
I tried to run get the program working as follows:
$ module load python $USER/deepvirfinder_env $USER/deepvirfinder_env/bin/activate $ pip install numpy theano keras scikit-learn $ pip install biopython
But when i run the program i get the following issues:
Using Theano backend. Traceback (most recent call last): File "/cvmfs/soft.HPC/easybuild/software/2017/Core/python/3.6.3/lib/python3.6/configparser.py", line 1138, in _unify_values sectiondict = self._sections[section] KeyError: 'blas'
During handling of the above exception, another exception occurred:
Traceback (most recent call last): File "/home/USER/deepvirfinder_env/lib/python3.6/site-packages/theano/configparser.py", line 168, in fetch_val_for_key return theano_cfg.get(section, option) File "/cvmfs/soft.HPC/easybuild/software/2017/Core/python/3.6.3/lib/python3.6/configparser.py", line 781, in get d = self._unify_values(section, vars) File "/cvmfs/soft.HPC/easybuild/software/2017/Core/python/3.6.3/lib/python3.6/configparser.py", line 1141, in _unify_values raise NoSectionError(section) configparser.NoSectionError: No section: 'blas'
During handling of the above exception, another exception occurred:
Traceback (most recent call last): File "/home/USER/deepvirfinder_env/lib/python3.6/site-packages/theano/configparser.py", line 328, in get delete_key=delete_key) File "/home/USER/deepvirfinder_env/lib/python3.6/site-packages/theano/configparser.py", line 172, in fetch_val_for_key raise KeyError(key) KeyError: 'blas.ldflags'
During handling of the above exception, another exception occurred:
Traceback (most recent call last): File "/home/USER/deepvirfinder_env/lib/python3.6/site-packages/theano/configdefaults.py", line 1250, in check_mkl_openmp import mkl ModuleNotFoundError: No module named 'mkl'
During handling of the above exception, another exception occurred:
Traceback (most recent call last): File "/home/USER/deepvirfinder_env/bin/DeepVirFinder/dvf.py", line 53, in
import keras
File "/home/USER/deepvirfinder_env/lib/python3.6/site-packages/keras/init.py", line 3, in
from . import utils
File "/home/USER/deepvirfinder_env/lib/python3.6/site-packages/keras/utils/init.py", line 6, in
from . import conv_utils
File "/home/USER/deepvirfinder_env/lib/python3.6/site-packages/keras/utils/conv_utils.py", line 9, in
from .. import backend as K
File "/home/USER/deepvirfinder_env/lib/python3.6/site-packages/keras/backend/init.py", line 1, in
from .load_backend import epsilon
File "/home/USER/deepvirfinder_env/lib/python3.6/site-packages/keras/backend/load_backend.py", line 87, in
from .theano_backend import *
File "/home/USER/deepvirfinder_env/lib/python3.6/site-packages/keras/backend/theano_backend.py", line 7, in
import theano
File "/home/USER/deepvirfinder_env/lib/python3.6/site-packages/theano/init.py", line 124, in
from theano.scan_module import (scan, map, reduce, foldl, foldr, clone,
File "/home/USER/deepvirfinder_env/lib/python3.6/site-packages/theano/scan_module/init.py", line 41, in
from theano.scan_module import scan_opt
File "/home/USER/deepvirfinder_env/lib/python3.6/site-packages/theano/scan_module/scan_opt.py", line 60, in
from theano import tensor, scalar
File "/home/USER/deepvirfinder_env/lib/python3.6/site-packages/theano/tensor/init.py", line 17, in
from theano.tensor import blas
File "/home/USER/deepvirfinder_env/lib/python3.6/site-packages/theano/tensor/blas.py", line 155, in
from theano.tensor.blas_headers import blas_header_text
File "/home/USER/deepvirfinder_env/lib/python3.6/site-packages/theano/tensor/blas_headers.py", line 987, in
if not config.blas.ldflags:
File "/home/USER/deepvirfinder_env/lib/python3.6/site-packages/theano/configparser.py", line 332, in get
val_str = self.default()
File "/home/USER/deepvirfinder_env/lib/python3.6/site-packages/theano/configdefaults.py", line 1430, in default_blas_ldflags
check_mkl_openmp()
File "/home/USER/deepvirfinder_env/lib/python3.6/site-packages/theano/configdefaults.py", line 1262, in check_mkl_openmp
""")
RuntimeError:
Could not import 'mkl'. Either install mkl-service with conda or set
MKL_THREADING_LAYER=GNU in your environment for MKL 2018.
If you have MKL 2017 install and are not in a conda environment you can set the Theano flag blas.check_openmp to False. Be warned that if you set this flag and don't set the appropriate environment or make sure you have the right version you will get wrong results.
Any thoughts?
Thanks